public int Launch()
{
CommonOptions commonOptions = _modeRunner.CommonOptions;
IDirectoryLocation outFolder = commonOptions.OutputDirectory;
var log = outFolder.GetFileLocation("CanvasLog.txt");
var error = outFolder.GetFileLocation("CanvasError.txt");
using (ILogger logger = new Logger(log, error))
{
try
{
logger.Info($"Running Canvas {_mode} {_version}");
logger.Info($"Command-line arguments: {string.Join(" ", _args)}");
using (ICheckpointRunner checkpointRunner =
GetCheckpointRunner(
logger,
outFolder,
commonOptions.StartCheckpoint,
commonOptions.StopCheckpoint,
commonOptions.WholeGenomeFasta))
{
IDirectoryLocation loggingFolder = outFolder.CreateSubdirectory(IsasFilePaths.LoggingFolderName);
IsasConfiguration config = IsasConfiguration.GetConfiguration();
IWorkManager workManager = new LocalWorkManager(logger, loggingFolder, 0, config.MaximumMemoryGB, config.MaximumHoursPerProcess);
_modeRunner.Run(logger, checkpointRunner, workManager);
}
}
catch (Exception e)
{
logger.Error($"Canvas workflow error: {e}");
return -1;
}
}
return 0;
}
public int Launch()
{
CommonOptions commonOptions = _modeRunner.CommonOptions;
IDirectoryLocation outFolder = commonOptions.OutputDirectory;
var log = outFolder.GetFileLocation("CanvasLog.txt");
var error = outFolder.GetFileLocation("CanvasError.txt");
using (ILogger logger = new Logger(log, error))
{
try
{
logger.Info($"Running Canvas {_mode} {_version}");
logger.Info($"Command-line arguments: {string.Join(" ", _args)}");
var checkpointRunner =
GetCheckpointRunner(
logger,
outFolder,
commonOptions.StartCheckpoint,
commonOptions.StopCheckpoint,
commonOptions.WholeGenomeFasta);
using (var manager = checkpointRunner.Manager)
{
IDirectoryLocation loggingFolder = outFolder.CreateSubdirectory("Logging");
IsasConfiguration config = IsasConfiguration.GetConfiguration();
IWorkManager workManager = new LocalWorkManager(logger, loggingFolder, 0, config.MaximumMemoryGB, config.MaximumHoursPerProcess);
_modeRunner.Run(logger, checkpointRunner, workManager);
manager.CheckFinalState();
}
}
catch (StopCheckpointFoundException) { }
catch (Exception e)
{
logger.Error($"Canvas workflow error: {e}");
return(-1);
}
}
return(0);
}
